Bruce W. Herr II1, Josef Hardi2, Ellen M. Quardokus1, Andreas Bueckle 1*, Lu Chen3, Fusheng Wang3, Anita R. Caron4, David Osumi-Sutherland 4, Mark A. Musen2, Katy Börner1*
* Corresponding authors
CCF.OWL v2.0.1 on NCBI BioPortal Ontology Browser
CCF.OWL v2.0.1 on EBI Ontology Lookup Service (OLS) Ontology Browser
We welcome others to join our effort in constructing a user-friendly and useful HRA. Please sign up for the ASCT+B Working Group at https://iu.co1.qualtrics.com/jfe/form/SV_bpaBhIr8XfdiNRH to receive updates and meeting invites.
We provide standard queries to a static version of the CCF API which includes CCF.OWL v2.0.1 and experimental data by five consortia made available as LOD. Note that counts for experimental data tissue blocks will be lower as in the paper because the database was compiled on June 23, 2022 and the paper reports data available on August 25, 2022. You can access the full data story here.
| Description | Count | Run Query |
|---|---|---|
| Number of RDF Triples in CCF.OWL v2.0.1 | 266,576 | Query |
| Human Reference Atlas Data | ||
| Biological structure | ||
| Number of Anatomical Structures | 2,619 | Query |
| Number of Anatomical Structures mapped to Uberon | 400 | Query |
| Number of Cell Types | 736 | Query |
| Number of Cell Types with unmapped IDs | 348 | Query |
| Number of LMHA Cell Types | 5 | Query |
| Number of Biomarkers | 1,540 | Query |
| Number of Biomarkers with HGNC IDs | 1,093 | Query |
| Number of Biomarkers with unmapped IDs | 447 | Query |
| Number of AS-AS Links | 3,116 | Query |
| Number of AS-CT Links | 10,331 | Query |
| Number of CT-B Links | 3,572 | Query |
| Spatial | ||
| Reference Organ Count | 53 | Query |
| 3D Reference Organ AS Count | 1,190 | Query |
| Number of Landmarks | 337 | Query |
| Experimental Data | ||
| Specimen | ||
| Donor Count | 137 | Query |
| Tissue Block Count | 359 | Query |
| Section Count | 561 | Query |
| Consortium Count | 5 | Query |
| Spatial | ||
| RUI Location Count | 350 | Query |
The RUI and EUI allow the 3D registration and subsequent exploration of tissue blocks in relation to the HRA (v1.2) reference organs. Video Tutorial 1 and a standard operating procedure ("Using the CCF Registration User Interface") illustrate their usage. Video Tutorial 2 shows how to validate a RUI location with the EUI.
Video Tutorial 1: RUI v3.0 Tutorial (watch on YouTube)
Video Tutorial 2: How to double-check a RUI registration with the EUI (watch on YouTube)
The CCF Organ VR Gallery is an immersive application that allows users to view, explore, and analyze 3D reference organs, anatomical structures, and cell types, in an integrated virtual reality (VR) environment. More information about this project can be found be found on the CCF Organ VR Gallery on the CCF Portal. A video demo is available below.
Video Demo: Features of the CCF Organ VR Gallery v0.5 (watch on YouTube)